The Sky Took Us

Kris Argentia is a 16-year-old math prodigy living in Toronto with her sister, Antoinette, and their mother, Sarah. When a black orb appears downtown, flashing strange mathematical patterns, millions of people suddenly disappear, including her mother. Soon, more orbs appear in major cities around the world.
Kris is recruited to join an international think tank, the M-team, based at a military base outside New York City. Alongside her PhD supervisor, Nate, and an intelligence operative named Toor, she tries to make sense of the patterns coming from the orbs. The work becomes more urgent as it becomes clear that the message is meant for her through her dreams.
She attempts to communicate directly with one of the orbs, but it fails. Back at the base, tensions rise, and after an argument involving Toor's son Ari, Antoinette is left in a coma.
With time running out, Kris returns to the problem and makes a breakthrough in the alien code, tied to her recent solution of the Riemann hypothesis, one of the greatest unsolved problems in mathematics. The team is finally able to communicate with the orbs, but Kris is the one who connects with them to bring the vanished back.
In the end, Kris is given a choice: go with the orbs or return to her family. She chooses to come back to her family, asking them to help her sister. Antoinette wakes up.